Growing concern about the quantity and diversity of by-catch species caught in the bottom trawling nets of crustacean fisheries led us to compare the quantity of by-catch recorded in Chilean and Costa Rican deep-water shrimp fisheries by year, latitude, and bathymetry. We analyzed catches from 2143 trawl hauls between 2004 and 2009 from the fisheries of the northern nylon shrimp, Heterocarpus vicarius, and the kolibri shrimp, Solenocera agassizii, off Costa Rica and the Chilean nylon shrimp, Heterocarpus reedi, off Chile. A catch index was estimated to determine the quantity of by-catch retained for each kilogram of shrimp. The by-catch associated with the shrimp fisheries of Costa Rica and Chile was mainly fishes and crustaceans; by-catch species diversity was considerably higher in Costa Rica compared to that of Chile. In Chile, catches of H. reedi and by-catch were greater in the central and southern zone, whereas in Costa Rica, catches of shrimp (H. vicarius, S. agassizii) and by-catch were higher in the central zone. In terms of bathymetry, the largest catches of shrimp and by-catch came from the deep stratum (between 251 and 400 m) for both countries; the by-catch was noticeably larger in this stratum in Costa Rica. The catch index revealed that for every 1 kg of shrimp caught in Costa Rica, 5.7 kg of by-catch were caught; in Chile, this ratio was 1.1:1. However, the projected global by-catch was considerably higher for the fishery for H. reedi than for that of H. vicarius, which is related to the landed volumes of the target species in Costa Rica and Chile. The encouraging results in the H. reedi-fishery concerning technical measures to reduce by-catch and discards rates should be also considered for Central American deep-water shrimp fisheries.